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are you running the correct batteries ? if you’re putting gel or possibly some agm batteries under your bonnet the lifespan will dramatically decrease check with manufacturer specifications , also if your 2nd batt is next to your turbo you could try putting in a heat shield around it.
have you got a volt gauge on both batteries independently so you can see when the isolator is charging your aux batt and see what your aux batt volts are once it disconnects maybe its not getting enough charge and is getting damaged that way
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